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Items: 47

1.

Comments on the model parameters in "SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models".

Zafar H, Tzen A, Navin N, Chen K, Nakhleh L.

Genome Biol. 2019 May 16;20(1):95. doi: 10.1186/s13059-019-1692-5. No abstract available.

2.

Somatic Trp53 mutations differentially drive breast cancer and evolution of metastases.

Zhang Y, Xiong S, Liu B, Pant V, Celii F, Chau G, Elizondo-Fraire AC, Yang P, You MJ, El-Naggar AK, Navin NE, Lozano G.

Nat Commun. 2018 Sep 27;9(1):3953. doi: 10.1038/s41467-018-06146-9.

3.

Resident Breast T Cells: The Troops Are Already There.

Schalck A, Bernatchez C, Navin N.

Trends Mol Med. 2018 Oct;24(10):821-822. doi: 10.1016/j.molmed.2018.07.006. Epub 2018 Aug 1.

4.

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing.

Kim C, Gao R, Sei E, Brandt R, Hartman J, Hatschek T, Crosetto N, Foukakis T, Navin NE.

Cell. 2018 May 3;173(4):879-893.e13. doi: 10.1016/j.cell.2018.03.041. Epub 2018 Apr 19.

5.

Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing.

Casasent AK, Schalck A, Gao R, Sei E, Long A, Pangburn W, Casasent T, Meric-Bernstam F, Edgerton ME, Navin NE.

Cell. 2018 Jan 11;172(1-2):205-217.e12. doi: 10.1016/j.cell.2017.12.007. Epub 2018 Jan 4.

6.

SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models.

Zafar H, Tzen A, Navin N, Chen K, Nakhleh L.

Genome Biol. 2017 Sep 19;18(1):178. doi: 10.1186/s13059-017-1311-2.

7.

Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer.

Gao R, Kim C, Sei E, Foukakis T, Crosetto N, Chan LK, Srinivasan M, Zhang H, Meric-Bernstam F, Navin N.

Nat Commun. 2017 Aug 9;8(1):228. doi: 10.1038/s41467-017-00244-w.

8.

Mutational Heterogeneity in APC and KRAS Arises at the Crypt Level and Leads to Polyclonality in Early Colorectal Tumorigenesis.

Gausachs M, Borras E, Chang K, Gonzalez S, Azuara D, Delgado Amador A, Lopez-Doriga A, San Lucas FA, Sanjuan X, Paules MJ, Taggart MW, Davies GE, Ehli EA, Fowler J, Moreno V, Pineda M, You YN, Lynch PM, Lazaro C, Navin NE, Scheet PA, Hawk ET, Capella G, Vilar E.

Clin Cancer Res. 2017 Oct 1;23(19):5936-5947. doi: 10.1158/1078-0432.CCR-17-0821. Epub 2017 Jun 23.

9.

Single-cell DNA sequencing reveals a late-dissemination model in metastatic colorectal cancer.

Leung ML, Davis A, Gao R, Casasent A, Wang Y, Sei E, Vilar E, Maru D, Kopetz S, Navin NE.

Genome Res. 2017 Aug;27(8):1287-1299. doi: 10.1101/gr.209973.116. Epub 2017 May 25.

10.

Tumor evolution: Linear, branching, neutral or punctuated?

Davis A, Gao R, Navin N.

Biochim Biophys Acta Rev Cancer. 2017 Apr;1867(2):151-161. doi: 10.1016/j.bbcan.2017.01.003. Epub 2017 Jan 19. Review.

11.

Genome evolution in ductal carcinoma in situ: invasion of the clones.

Casasent AK, Edgerton M, Navin NE.

J Pathol. 2017 Jan;241(2):208-218. doi: 10.1002/path.4840. Epub 2016 Nov 27. Review.

12.

Single-cell analysis at the threshold.

Chen X, Love JC, Navin NE, Pachter L, Stubbington MJ, Svensson V, Sweedler JV, Teichmann SA.

Nat Biotechnol. 2016 Nov 8;34(11):1111-1118. doi: 10.1038/nbt.3721. No abstract available.

PMID:
27824834
13.

Punctuated copy number evolution and clonal stasis in triple-negative breast cancer.

Gao R, Davis A, McDonald TO, Sei E, Shi X, Wang Y, Tsai PC, Casasent A, Waters J, Zhang H, Meric-Bernstam F, Michor F, Navin NE.

Nat Genet. 2016 Oct;48(10):1119-30. doi: 10.1038/ng.3641. Epub 2016 Aug 15.

14.

Analyzing tumor heterogeneity and driver genes in single myeloid leukemia cells with SBCapSeq.

Mann KM, Newberg JY, Black MA, Jones DJ, Amaya-Manzanares F, Guzman-Rojas L, Kodama T, Ward JM, Rust AG, van der Weyden L, Yew CC, Waters JL, Leung ML, Rogers K, Rogers SM, McNoe LA, Selvanesan L, Navin N, Jenkins NA, Copeland NG, Mann MB.

Nat Biotechnol. 2016 Sep;34(9):962-72. doi: 10.1038/nbt.3637. Epub 2016 Aug 1.

15.

Genotyping tumor clones from single-cell data.

Navin NE, Chen K.

Nat Methods. 2016 Jun 29;13(7):555-6. doi: 10.1038/nmeth.3903. No abstract available.

PMID:
27355792
16.

Computing tumor trees from single cells.

Davis A, Navin NE.

Genome Biol. 2016 May 26;17(1):113. doi: 10.1186/s13059-016-0987-z.

17.

Monovar: single-nucleotide variant detection in single cells.

Zafar H, Wang Y, Nakhleh L, Navin N, Chen K.

Nat Methods. 2016 Jun;13(6):505-7. doi: 10.1038/nmeth.3835. Epub 2016 Apr 18.

18.

Corrigendum: Genome-wide copy number analysis of single cells.

Baslan T, Kendall J, Rodgers L, Cox H, Riggs M, Stepansky A, Troge J, Ravi K, Esposito D, Lakshmi B, Wigler M, Navin N, Hicks J.

Nat Protoc. 2016 Mar;11(3):616. doi: 10.1038/nprot0316.616b. Epub 2016 Feb 25. No abstract available.

PMID:
26914320
19.

Highly multiplexed targeted DNA sequencing from single nuclei.

Leung ML, Wang Y, Kim C, Gao R, Jiang J, Sei E, Navin NE.

Nat Protoc. 2016 Feb;11(2):214-235. doi: 10.1038/nprot.2016.005. Epub 2016 Jan 7.

20.

The first five years of single-cell cancer genomics and beyond.

Navin NE.

Genome Res. 2015 Oct;25(10):1499-507. doi: 10.1101/gr.191098.115.

21.

Toward understanding and exploiting tumor heterogeneity.

Alizadeh AA, Aranda V, Bardelli A, Blanpain C, Bock C, Borowski C, Caldas C, Califano A, Doherty M, Elsner M, Esteller M, Fitzgerald R, Korbel JO, Lichter P, Mason CE, Navin N, Pe'er D, Polyak K, Roberts CW, Siu L, Snyder A, Stower H, Swanton C, Verhaak RG, Zenklusen JC, Zuber J, Zucman-Rossi J.

Nat Med. 2015 Aug;21(8):846-53. doi: 10.1038/nm.3915.

22.

Delineating cancer evolution with single-cell sequencing.

Navin NE.

Sci Transl Med. 2015 Jul 15;7(296):296fs29. doi: 10.1126/scitranslmed.aac8319.

23.

Advances and applications of single-cell sequencing technologies.

Wang Y, Navin NE.

Mol Cell. 2015 May 21;58(4):598-609. doi: 10.1016/j.molcel.2015.05.005. Review.

24.

SNES: single nucleus exome sequencing.

Leung ML, Wang Y, Waters J, Navin NE.

Genome Biol. 2015 Mar 25;16:55. doi: 10.1186/s13059-015-0616-2.

25.

Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations.

Malhotra A, Wang Y, Waters J, Chen K, Meric-Bernstam F, Hall IM, Navin NE.

Genome Med. 2015 Jan 28;7(1):6. doi: 10.1186/s13073-015-0127-5. eCollection 2015.

26.

Cancer genomics: one cell at a time.

Navin NE.

Genome Biol. 2014 Aug 30;15(8):452. doi: 10.1186/s13059-014-0452-9. Review.

27.

Clonal evolution in breast cancer revealed by single nucleus genome sequencing.

Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE.

Nature. 2014 Aug 14;512(7513):155-60. doi: 10.1038/nature13600. Epub 2014 Jul 30.

28.

Tumor evolution in response to chemotherapy: phenotype versus genotype.

Navin NE.

Cell Rep. 2014 Feb 13;6(3):417-9. doi: 10.1016/j.celrep.2014.01.035.

29.

BreakTrans: uncovering the genomic architecture of gene fusions.

Chen K, Navin NE, Wang Y, Schmidt HK, Wallis JW, Niu B, Fan X, Zhao H, McLellan MD, Hoadley KA, Mardis ER, Ley TJ, Perou CM, Wilson RK, Ding L.

Genome Biol. 2013 Aug 23;14(8):R87. doi: 10.1186/gb-2013-14-8-r87.

30.

Genome-wide copy number analysis of single cells.

Baslan T, Kendall J, Rodgers L, Cox H, Riggs M, Stepansky A, Troge J, Ravi K, Esposito D, Lakshmi B, Wigler M, Navin N, Hicks J.

Nat Protoc. 2012 May 3;7(6):1024-41. doi: 10.1038/nprot.2012.039. Erratum in: Nat Protoc. 2016 Mar;11(3):616.

31.

Insight into the heterogeneity of breast cancer through next-generation sequencing.

Russnes HG, Navin N, Hicks J, Borresen-Dale AL.

J Clin Invest. 2011 Oct;121(10):3810-8. doi: 10.1172/JCI57088. Epub 2011 Oct 3. Review.

32.

Identification of PHLPP1 as a tumor suppressor reveals the role of feedback activation in PTEN-mutant prostate cancer progression.

Chen M, Pratt CP, Zeeman ME, Schultz N, Taylor BS, O'Neill A, Castillo-Martin M, Nowak DG, Naguib A, Grace DM, Murn J, Navin N, Atwal GS, Sander C, Gerald WL, Cordon-Cardo C, Newton AC, Carver BS, Trotman LC.

Cancer Cell. 2011 Aug 16;20(2):173-86. doi: 10.1016/j.ccr.2011.07.013.

33.

Toward an integrated knowledge environment to support modern oncology.

Blake PM, Decker DA, Glennon TM, Liang YM, Losko S, Navin N, Suh KS.

Cancer J. 2011 Jul-Aug;17(4):257-63. doi: 10.1097/PPO.0b013e31822c390b. Review.

PMID:
21799334
34.

Future medical applications of single-cell sequencing in cancer.

Navin N, Hicks J.

Genome Med. 2011 May 31;3(5):31. doi: 10.1186/gm247.

35.

Tumour evolution inferred by single-cell sequencing.

Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie WR, Hicks J, Wigler M.

Nature. 2011 Apr 7;472(7341):90-4. doi: 10.1038/nature09807. Epub 2011 Mar 13.

36.

Tracing the tumor lineage.

Navin NE, Hicks J.

Mol Oncol. 2010 Jun;4(3):267-83. doi: 10.1016/j.molonc.2010.04.010. Epub 2010 May 5. Erratum in: Mol Oncol. 2011 Jun;5(3):302.

37.

Inferring tumor progression from genomic heterogeneity.

Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A, Hicks J, Wigler M.

Genome Res. 2010 Jan;20(1):68-80. doi: 10.1101/gr.099622.109. Epub 2009 Nov 10.

38.

Probing WW Domains to Uncover and Refine Determinants of Specificity in Ligand Recognition.

Espanel X, Navin N, Kato Y, Tanokura M, Sudol M.

Cytotechnology. 2003 Nov;43(1-3):105-11. doi: 10.1023/B: CYTO.0000039913.56708.06.

39.

Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA).

Grubor V, Krasnitz A, Troge JE, Meth JL, Lakshmi B, Kendall JT, Yamrom B, Alex G, Pai D, Navin N, Hufnagel LA, Lee YH, Cook K, Allen SL, Rai KR, Damle RN, Calissano C, Chiorazzi N, Wigler M, Esposito D.

Blood. 2009 Feb 5;113(6):1294-303. doi: 10.1182/blood-2008-05-158865. Epub 2008 Oct 15.

40.

Computer vision syndrome: a study of the knowledge, attitudes and practices in Indian ophthalmologists.

Bali J, Navin N, Thakur BR.

Indian J Ophthalmol. 2007 Jul-Aug;55(4):289-94.

41.

Identification of alterations in DNA copy number in host stromal cells during tumor progression.

Pelham RJ, Rodgers L, Hall I, Lucito R, Nguyen KC, Navin N, Hicks J, Mu D, Powers S, Wigler M, Botstein D.

Proc Natl Acad Sci U S A. 2006 Dec 26;103(52):19848-53. Epub 2006 Dec 13.

42.

Novel patterns of genome rearrangement and their association with survival in breast cancer.

Hicks J, Krasnitz A, Lakshmi B, Navin NE, Riggs M, Leibu E, Esposito D, Alexander J, Troge J, Grubor V, Yoon S, Wigler M, Ye K, Børresen-Dale AL, Naume B, Schlicting E, Norton L, Hägerström T, Skoog L, Auer G, Månér S, Lundin P, Zetterberg A.

Genome Res. 2006 Dec;16(12):1465-79.

43.

High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors.

Hicks J, Muthuswamy L, Krasnitz A, Navin N, Riggs M, Grubor V, Esposito D, Alexander J, Troge J, Wigler M, Maner S, Lundin P, Zetterberg A.

Cold Spring Harb Symp Quant Biol. 2005;70:51-63.

PMID:
16869738
44.

PROBER: oligonucleotide FISH probe design software.

Navin N, Grubor V, Hicks J, Leibu E, Thomas E, Troge J, Riggs M, Lundin P, Månér S, Sebat J, Zetterberg A, Wigler M.

Bioinformatics. 2006 Oct 1;22(19):2437-8. Epub 2006 Jun 1.

PMID:
16740623
45.

Large-scale copy number polymorphism in the human genome.

Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Månér S, Massa H, Walker M, Chi M, Navin N, Lucito R, Healy J, Hicks J, Ye K, Reiner A, Gilliam TC, Trask B, Patterson N, Zetterberg A, Wigler M.

Science. 2004 Jul 23;305(5683):525-8.

46.

Distribution of short paired duplications in mammalian genomes.

Thomas EE, Srebro N, Sebat J, Navin N, Healy J, Mishra B, Wigler M.

Proc Natl Acad Sci U S A. 2004 Jul 13;101(28):10349-54. Epub 2004 Jul 6.

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